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Protein

CRISPR-associated endonuclease Cas1

Gene

ygbT

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids) (PubMed:21255106, PubMed:24920831, PubMed:24793649). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The Cas1-Cas2 complex is involved in CRISPR adaptation, the first stage of CRISPR immunity, being required for the addition/removal of CRISPR spacers at the leader end of the CRISPR locus (PubMed:24920831, PubMed:25707795, PubMed:24793649). The Cas1-Cas2 complex introduces staggered nicks into both strands of the CRISPR array near the leader repeat and joins the 5'-ends of the repeat strands with the 3'-ends of the new spacer sequence (PubMed:24920831). Spacer DNA integration requires supercoiled target DNA and 3'-OH ends on the inserted (spacer) DNA and probably initiates with a nucleophilic attack of the C 3'-OH end of the protospacer on the minus strand of the first repeat sequence (PubMed:25707795). Expression of Cas1-Cas2 in a strain lacking both genes permits spacer acquisition (PubMed:24793649, PubMed:24920831). Non-specifically binds DNA; the Cas1-Cas2 complex preferentially binds CRISPR-locus DNA (PubMed:24793649). Highest binding is seen to a dual forked DNA complex with 3'-overhangs and a protospacer-adjacent motif-complement specifically positioned (PubMed:26478180). The protospacer DNA lies across a flat surface extending from 1 Cas1 dimer, across the Cas2 dimer and contacting the other Cas1 dimer; the 23 bp-long ds section of the DNA is bracketed by 1 Tyr-22 from each of the Cas1 dimers (PubMed:26478180, PubMed:26503043). Cas1 cuts within the 3'-overhang, to generate a 33-nucleotide DNA that is probably incorporated into the CRISPR leader by a cut-and-paste mechanism (PubMed:26478180). Cas1 alone endonucleolytically cleaves linear ssRNA, ssDNA and short (34 base) dsDNA as well as branched DNA substrates such as Holliday junctions, replication forks and 5'-flap DNA substrates (PubMed:21219465). In vitro catalyzes a concerted transesterification reaction on branched DNA, as would be expected during integration of protospacers into the CRISPR leader sequence; Cas2 is not required in vitro. This reaction requires a 3'-OH group at the branch point (PubMed:26284603). Genetic interactions suggest Cas1 interacts with components of the RecBC and RuvB DNA repair systems (PubMed:21219465).7 Publications

Cofactori

Mg2+3 PublicationsNote: Protospacer integration in vitro also occurs with Mn2+ and also requires low concentrations of KCl (PubMed:25707795). The transesterification function works equally well with Mg2+, Mn2+ or Co2+ in vitro (PubMed:26284603).2 Publications

Enzyme regulationi

Nuclease activity partially inhibited by CasE (PubMed:21219465).1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei1412 Publications1
Metal bindingi141MagnesiumBy similarity1
Active sitei2082 Publications1
Metal bindingi208MagnesiumBy similarity1
Active sitei2212 Publications1
Metal bindingi221MagnesiumBy similarity1

GO - Molecular functioni

  • 5'-flap endonuclease activity Source: EcoCyc
  • crossover junction endodeoxyribonuclease activity Source: EcoCyc
  • DNA binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoCyc
  • defense response to virus Source: UniProtKB-HAMAP
  • DNA repair Source: UniProtKB-KW
  • maintenance of CRISPR repeat elements Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Hydrolase, Nuclease

Keywords - Biological processi

Antiviral defense, DNA damage, DNA repair

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:G7425-MONOMER.
ECOL316407:JW2725-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
CRISPR-associated endonuclease Cas1 (EC:3.1.-.-)
Gene namesi
Name:ygbT
Synonyms:cas1
Ordered Locus Names:b2755, JW2725
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13114. ygbT.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Not essential. Increased sensitivity to MMC and UV light; double ygbT-ruvA, ruvB or ruvC disruptions have no further phenotype suggesting Cas1 functions in the same DNA repair pathway (PubMed:21219465). Function in DNA repair also seems to require CRISPRs (PubMed:21219465). Cells elongate after 2 hours growth in MMC; they are even longer in double ygbT-ruvA, ruvB or ruvC disruptions, suggesting Cas1 may also function in chromosome segregation (PubMed:21219465). Loss of plasmid silencing (PubMed:21255106).2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi22Y → A: Slightly decreased spacer acquisition in vivo. 2 Publications1
Mutagenesisi22Y → F: Nearly wild-type spacer acquisition in vivo. 1 Publication1
Mutagenesisi41R → E: Dramatically decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi59R → A: Loss of spacer acquisition in vivo, decreased protospacer binding. 1 Publication1
Mutagenesisi59R → D: Dramatically decreased spacer acquisition in vitro, 250-fold decreased affinity for protospacer DNA. 1 Publication1
Mutagenesisi66R → D: Dramatically decreased spacer acquisition in vitro, 250-fold decreased affinity for protospacer DNA. 1 Publication1
Mutagenesisi66R → E: Dramatically decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi84R → A: Decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi84R → E: Dramatically decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi141E → A: No cleavage of any substrates, no restoration of UV or mitomycin C (MMC) resistance (PubMed:21219465). Loss of spacer acquisition in vivo (PubMed:24793649). 2 Publications1
Mutagenesisi149Y → A: No effect on in vitro protospacer integration. 1 Publication1
Mutagenesisi165Y → A: No effect on in vitro protospacer integration (PubMed:25707795). Alone significantly decreased protospacer acquisition in vivo (PubMed:26478180). Loss of protospacer acquisition, decreased protospacer binding; in association with A-170, significantly decreased protospacer binding; in association with A-217 (PubMed:26478180). 2 Publications1
Mutagenesisi170W → A: Alone significantly decreased protospacer acquisition in vivo (PubMed:26478180). Decreased protospacer binding; in association with A-170 (PubMed:26478180). 1 Publication1
Mutagenesisi184T → A: No cleavage of any substrates. 1 Publication1
Mutagenesisi188Y → A: Partial inhibition of cleavage (PubMed:21219465). No effect on in vitro protospacer integration (PubMed:25707795). Significantly decreased protospacer acquisition in vivo (PubMed:26478180). 3 Publications1
Mutagenesisi208H → A: No cleavage of any substrates, no restoration of UV or MMC resistance (PubMed:21219465). Loss of spacer acquisition in vivo (PubMed:24793649, PubMed:25707795, PubMed:26478180). 4 Publications1
Mutagenesisi211K → A: No cleavage of any substrates. 1 Publication1
Mutagenesisi217Y → A: No effect on in vitro protospacer integration (PubMed:25707795). Alone significantly decreased protospacer acquisition in vivo (PubMed:26478180). Significantly decreased protospacer binding; in association with A-165 (PubMed:26478180). 2 Publications1
Mutagenesisi218D → A: No cleavage of any substrates, no restoration of UV or MMC resistance (PubMed:21219465). Loss of spacer acquisition in vivo (PubMed:24793649). 2 Publications1
Mutagenesisi221D → A: No cleavage of any substrates (PubMed:21219465). Loss of spacer acquisition in vivo (PubMed:24793649, PubMed:24920831, PubMed:25707795). No cleavage of CRISPR leader in preparation for spacer integration (PubMed:24920831). 4 Publications1
Mutagenesisi224K → A: No cleavage of any substrates (PubMed:21219465). Loss of spacer acquisition in vivo (PubMed:24793649, PubMed:25707795). 3 Publications1
Mutagenesisi245 – 248REVR → AEVA: Loss of spacer acquisition in vivo. 1 Publication4
Mutagenesisi245R → A: No effect on spacer acquisition. 1 Publication1
Mutagenesisi245R → D: Decreased spacer acquisition. 1 Publication1
Mutagenesisi245R → E: Dramatically decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi248R → E: Dramatically decreased spacer acquisition in vivo. 1 Publication1
Mutagenesisi252R → A: No effect on spacer acquisition. 1 Publication1
Mutagenesisi252R → E: Loss of spacer acquisition, no Cas1-Cas2 complex formation, loss of CRISPR DNA-binding by complex. Protein is stable and dimerizes. 1 Publication1
Mutagenesisi256 – 259RSSK → ASSA: Loss of spacer acquisition in vivo. 1 Publication4
Mutagenesisi256R → A: No effect on spacer acquisition. 1 Publication1
Mutagenesisi256R → E: Loss of spacer acquisition. 1 Publication1
Mutagenesisi282 – 305Missing : No effect on spacer acquisition, Cas1-Cas2 complex formation or CRISPR DNA-binding by complex. 1 PublicationAdd BLAST24
Mutagenesisi291I → G or R: No effect on spacer acquisition. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001693151 – 305CRISPR-associated endonuclease Cas1Add BLAST305

Proteomic databases

PaxDbiQ46896.
PRIDEiQ46896.

Expressioni

Inductioni

Repressed by H-NS (PubMed:20132443). Activated by LeuO (PubMed:19429622). Activated by the BaeSR two-component regulatory system, possibly due to envelope stress (PubMed:21255106). Part of the casABCDE-ygbT-ygbF operon (PubMed:19429622).3 Publications

Interactioni

Subunit structurei

Homodimer (PubMed:21219465). Part of the Cas1-Cas2 complex (PubMed:24920831, PubMed:24793649, PubMed:25707795, Ref. 11, PubMed:26478180, PubMed:26503043). Interacts with RecB, RecC, RuvB, CasC and CasE (PubMed:21219465). Forms a hexamer with 2 Cas1 dimers sandwiching a Cas2 dimer (PubMed:24793649, PubMed:26478180). The DNA lies across a flat surface extending from 1 Cas1 dimer, across the Cas2 dimer and contacting the other Cas1 dimer. Only 1 Cas1 protein from each dimer is catalytic, the other interacts with the Cas2 dimer and possibly target DNA (PubMed:26478180, PubMed:26503043).1 Publication6 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
yedVP763393EBI-1130209,EBI-554869

Protein-protein interaction databases

BioGridi4261582. 279 interactors.
DIPiDIP-12118N.
IntActiQ46896. 15 interactors.
STRINGi511145.b2755.

Structurei

Secondary structure

1305
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi11 – 13Combined sources3
Beta strandi17 – 20Combined sources4
Beta strandi22 – 28Combined sources7
Beta strandi31 – 36Combined sources6
Beta strandi37 – 39Combined sources3
Beta strandi41 – 43Combined sources3
Helixi46 – 48Combined sources3
Beta strandi50 – 54Combined sources5
Beta strandi58 – 60Combined sources3
Helixi62 – 70Combined sources9
Beta strandi74 – 79Combined sources6
Helixi80 – 82Combined sources3
Beta strandi85 – 90Combined sources6
Helixi95 – 107Combined sources13
Helixi109 – 124Combined sources16
Beta strandi130 – 132Combined sources3
Helixi134 – 156Combined sources23
Helixi167 – 169Combined sources3
Helixi170 – 172Combined sources3
Helixi175 – 197Combined sources23
Beta strandi206 – 208Combined sources3
Helixi214 – 223Combined sources10
Turni224 – 227Combined sources4
Helixi228 – 238Combined sources11
Helixi243 – 258Combined sources16
Helixi260 – 273Combined sources14
Beta strandi275 – 277Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3NKDX-ray1.95A/B1-305[»]
3NKEX-ray1.40A/B/C92-291[»]
4P6IX-ray2.30C/D/E/F1-305[»]
4QDLX-ray2.70A/B/C/D1-305[»]
5DLJX-ray2.60A/B/C/D2-281[»]
5DQTX-ray3.10A/B/C/D/I/J/K/L1-305[»]
5DQUX-ray4.50A/B/C/D1-305[»]
5DQZX-ray2.70A/B/C/D1-305[»]
5DS4X-ray3.20A/B/C/D1-305[»]
5DS5X-ray2.95A/B/C/D1-305[»]
5DS6X-ray3.35A/B/C/D1-305[»]
ProteinModelPortaliQ46896.
SMRiQ46896.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni96 – 278Sufficient for cleavage of ssRNA, ssDNA and Holliday junction DNAAdd BLAST183

Domaini

Substrate DNA-binding induces large structural changes that generate a surface for DNA-binding across the Cas2 dimer and formation of an optimal catalytic site (PubMed:26478180).1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105TZK. Bacteria.
COG1518. LUCA.
HOGENOMiHOG000015862.
InParanoidiQ46896.
KOiK15342.
OMAiIGDAGHR.

Family and domain databases

CDDicd09719. Cas1_I-E. 1 hit.
HAMAPiMF_01470. Cas1. 1 hit.
InterProiIPR033641. Cas1_I-E.
IPR002729. CRISPR-assoc_Cas1.
IPR019851. CRISPR-assoc_Cas1_ECOLI.
[Graphical view]
PfamiPF01867. Cas_Cas1. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00287. cas1. 2 hits.
TIGR03638. cas1_ECOLI. 1 hit.

Sequencei

Sequence statusi: Complete.

Q46896-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTWLPLNPIP LKDRVSMIFL QYGQIDVIDG AFVLIDKTGI RTHIPVGSVA
60 70 80 90 100
CIMLEPGTRV SHAAVRLAAQ VGTLLVWVGE AGVRVYASGQ PGGARSDKLL
110 120 130 140 150
YQAKLALDED LRLKVVRKMF ELRFGEPAPA RRSVEQLRGI EGSRVRATYA
160 170 180 190 200
LLAKQYGVTW NGRRYDPKDW EKGDTINQCI SAATSCLYGV TEAAILAAGY
210 220 230 240 250
APAIGFVHTG KPLSFVYDIA DIIKFDTVVP KAFEIARRNP GEPDREVRLA
260 270 280 290 300
CRDIFRSSKT LAKLIPLIED VLAAGEIQPP APPEDAQPVA IPLPVSLGDA

GHRSS
Length:305
Mass (Da):33,194
Last modified:November 1, 1996 - v1
Checksum:i01A31BA98453D8A5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29579 Genomic DNA. Translation: AAA69265.1.
U00096 Genomic DNA. Translation: AAC75797.1.
AP009048 Genomic DNA. Translation: BAE76832.1.
PIRiG65056.
RefSeqiNP_417235.1. NC_000913.3.
WP_000220066.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75797; AAC75797; b2755.
BAE76832; BAE76832; BAE76832.
GeneIDi947228.
KEGGiecj:JW2725.
eco:b2755.
PATRICi32120920. VBIEscCol129921_2852.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U29579 Genomic DNA. Translation: AAA69265.1.
U00096 Genomic DNA. Translation: AAC75797.1.
AP009048 Genomic DNA. Translation: BAE76832.1.
PIRiG65056.
RefSeqiNP_417235.1. NC_000913.3.
WP_000220066.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3NKDX-ray1.95A/B1-305[»]
3NKEX-ray1.40A/B/C92-291[»]
4P6IX-ray2.30C/D/E/F1-305[»]
4QDLX-ray2.70A/B/C/D1-305[»]
5DLJX-ray2.60A/B/C/D2-281[»]
5DQTX-ray3.10A/B/C/D/I/J/K/L1-305[»]
5DQUX-ray4.50A/B/C/D1-305[»]
5DQZX-ray2.70A/B/C/D1-305[»]
5DS4X-ray3.20A/B/C/D1-305[»]
5DS5X-ray2.95A/B/C/D1-305[»]
5DS6X-ray3.35A/B/C/D1-305[»]
ProteinModelPortaliQ46896.
SMRiQ46896.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261582. 279 interactors.
DIPiDIP-12118N.
IntActiQ46896. 15 interactors.
STRINGi511145.b2755.

Proteomic databases

PaxDbiQ46896.
PRIDEiQ46896.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75797; AAC75797; b2755.
BAE76832; BAE76832; BAE76832.
GeneIDi947228.
KEGGiecj:JW2725.
eco:b2755.
PATRICi32120920. VBIEscCol129921_2852.

Organism-specific databases

EchoBASEiEB2915.
EcoGeneiEG13114. ygbT.

Phylogenomic databases

eggNOGiENOG4105TZK. Bacteria.
COG1518. LUCA.
HOGENOMiHOG000015862.
InParanoidiQ46896.
KOiK15342.
OMAiIGDAGHR.

Enzyme and pathway databases

BioCyciEcoCyc:G7425-MONOMER.
ECOL316407:JW2725-MONOMER.

Miscellaneous databases

PROiQ46896.

Family and domain databases

CDDicd09719. Cas1_I-E. 1 hit.
HAMAPiMF_01470. Cas1. 1 hit.
InterProiIPR033641. Cas1_I-E.
IPR002729. CRISPR-assoc_Cas1.
IPR019851. CRISPR-assoc_Cas1_ECOLI.
[Graphical view]
PfamiPF01867. Cas_Cas1. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00287. cas1. 2 hits.
TIGR03638. cas1_ECOLI. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiCAS1_ECOLI
AccessioniPrimary (citable) accession number: Q46896
Secondary accession number(s): Q2MA74
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 2001
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.